An alter ego was an individual's alternative personality.
The puppet Balok was an alter ego for the diminutive real Balok. In 2266, drawing a comparison from Earth culture, Balok described the puppet as Mister Hyde and himself as Jekyll. As a thing meant to frighten the USS Enterprise crew, the puppet Balok was effective. (TOS: "The Corbomite Maneuver")
In 2373, The Doctor expressed his relief that his more violent alter ego didn't do any permanent damage. (VOY: "Darkling")